biostudies-literatureUnknownShuken SRNIA NIH HHSNIGMS NIH HHSExisting targeted mass spectrometry methods require synthetic standard peptides, manual scan scheduling, or data libraries to quantify target proteins. Here we present GoDig-LiF, which uses spectra and retention times predicted by the Prosit-TMT model in place of data libraries, enabling targeted proteomics with only a tandem mass tag-labeled sample, target list, and mass spectrometer. We applied GoDig-LiF to the quantification of mutated proteins in cancer cell lines, including KRAS G13D.bioRxiv : the preprint server for biology2025.09.10.675407https://www.ebi.ac.uk/biostudies/studies/S-EPMC12458936biostudies-literatureLibrary-Free Multiplexed Targeted Proteomics Enables Quantitative Protein-Level Genotyping.PMC12458936K99 AG088297R01 GM067945Shuken SRGygi SPfalseLibrary-Free Multiplexed Targeted Proteomics Enables Quantitative Protein-Level Genotyping.Existing targeted mass spectrometry methods require synthetic standard peptides, manual scan scheduling, or data libraries to quantify target proteins. Here we present GoDig-LiF, which uses spectra and retention times predicted by the Prosit-TMT model in place of data libraries, enabling targeted proteomics with only a tandem mass tag-labeled sample, target list, and mass spectrometer. We applied GoDig-LiF to the quantification of mutated proteins in cancer cell lines, including KRAS G13D.2025-01-01T00:00:00Z2025 Sep2026-05-04T03:20:57.382Z2026-05-04T03:14:25.384ZS-EPMC124589364100100410.1101/2025.09.10.675407